/**
 * @file src/TracebackMotif.cpp
 *
 * @date 14-may-2013
 *
 * @author Youri Hoogstrate
 * @author Lisa Yu
 *
 * @section LICENSE
 * yh-kt-fold can predict RNA 2D structures including K-turns.
 * Copyright (C) 2012-2013 Youri Hoogstrate
 *
 * This file is part of yh-kt-fold.
 *
 * yh-kt-fold is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * yh-kt-fold is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 */



#include "main.h"



/**
 * @brief Stores motifs used for the traceback algorithm, K-Turns for example.
 *
 * @section DESCRIPTION
 * Stores a traceback Path with additional jumps
 *
 * @date 25-may-2013
 */
class TracebackMotif
{
	private:
		bool tracebackDirectionForward;									// True -> forwards && False -> backwars
		
		int tracebackStackTop;
		int tracebackStack[16][2];										// 16 is max length of motif, can be changed but takes more memory <- should be changed by MALLOC
		
	public:
		void init(int arg_bonds[], int arg_size5p, int arg_size3p, bool arg_direction);
		bool pop(int *i, int *j);
};
